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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:MTMR2-ATP2C1 (FusionGDB2 ID:55747)

Fusion Gene Summary for MTMR2-ATP2C1

check button Fusion gene summary
Fusion gene informationFusion gene name: MTMR2-ATP2C1
Fusion gene ID: 55747
HgeneTgene
Gene symbol

MTMR2

ATP2C1

Gene ID

8898

27032

Gene namemyotubularin related protein 2ATPase secretory pathway Ca2+ transporting 1
SynonymsCMT4B|CMT4B1ATP2C1A|BCPM|HHD|PMR1|SPCA1|hSPCA1
Cytomap

11q21

3q22.1

Type of geneprotein-codingprotein-coding
Descriptionmyotubularin-related protein 2phosphatidylinositol-3,5-bisphosphate 3-phosphatasephosphatidylinositol-3-phosphatasephosphatidylinositol-3-phosphate phosphatasephosphoinositide-3-phosphatasecalcium-transporting ATPase type 2C member 1ATP-dependent Ca(2+) pump PMR1ATPase 2C1ATPase, Ca(2+)-sequesteringATPase, Ca++ transporting, type 2C, member 1HUSSY-28secretory pathway Ca2+/Mn2+ ATPase 1
Modification date2020032820200313
UniProtAcc

Q13614

P98194

Ensembl transtripts involved in fusion geneENST00000346299, ENST00000352297, 
ENST00000393223, ENST00000409459, 
ENST00000484818, 		ENST00000328560, 
ENST00000359644, ENST00000393221, 
ENST00000422190, ENST00000428331, 
ENST00000504381, ENST00000504948, 
ENST00000505330, ENST00000507488, 
ENST00000508532, ENST00000510168, 
ENST00000513801, ENST00000533801, 
ENST00000509150, 
Fusion gene scores* DoF score8 X 9 X 7=50411 X 11 X 6=726
# samples 1312
** MAII scorelog2(13/504*10)=-1.95491211047146
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(12/726*10)=-2.59693514238723
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MTMR2 [Title/Abstract] AND ATP2C1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMTMR2(95657037)-ATP2C1(130649258), # samples:1
Anticipated loss of major functional domain due to fusion event.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneMTMR2

GO:0046856

phosphatidylinositol dephosphorylation

12668758

HgeneMTMR2

GO:0060304

regulation of phosphatidylinositol dephosphorylation

16787938

TgeneATP2C1

GO:0006816

calcium ion transport

12810057

TgeneATP2C1

GO:0006874

cellular calcium ion homeostasis

12810057


check buttonFusion gene breakpoints across MTMR2 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across ATP2C1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChiTaRS5.0N/ADB155299MTMR2chr11

95657037

-ATP2C1chr3

130649258

+


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Fusion Gene ORF analysis for MTMR2-ATP2C1

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
5CDS-5UTRENST00000346299ENST00000328560MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5CDS-5UTRENST00000346299ENST00000359644MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5CDS-5UTRENST00000346299ENST00000393221MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5CDS-5UTRENST00000346299ENST00000422190MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5CDS-5UTRENST00000346299ENST00000428331MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5CDS-5UTRENST00000346299ENST00000504381MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5CDS-5UTRENST00000346299ENST00000504948MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5CDS-5UTRENST00000346299ENST00000505330MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5CDS-5UTRENST00000346299ENST00000507488MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5CDS-5UTRENST00000346299ENST00000508532MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5CDS-5UTRENST00000346299ENST00000510168MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5CDS-5UTRENST00000346299ENST00000513801MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5CDS-5UTRENST00000346299ENST00000533801MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5CDS-intronENST00000346299ENST00000509150MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000352297ENST00000328560MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000352297ENST00000359644MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000352297ENST00000393221MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000352297ENST00000422190MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000352297ENST00000428331MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000352297ENST00000504381MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000352297ENST00000504948MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000352297ENST00000505330MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000352297ENST00000507488MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000352297ENST00000508532MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000352297ENST00000510168MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000352297ENST00000513801MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000352297ENST00000533801MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000393223ENST00000328560MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000393223ENST00000359644MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000393223ENST00000393221MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000393223ENST00000422190MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000393223ENST00000428331MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000393223ENST00000504381MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000393223ENST00000504948MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000393223ENST00000505330MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000393223ENST00000507488MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000393223ENST00000508532MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000393223ENST00000510168MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000393223ENST00000513801MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000393223ENST00000533801MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000409459ENST00000328560MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000409459ENST00000359644MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000409459ENST00000393221MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000409459ENST00000422190MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000409459ENST00000428331MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000409459ENST00000504381MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000409459ENST00000504948MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000409459ENST00000505330MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000409459ENST00000507488MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000409459ENST00000508532MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000409459ENST00000510168MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000409459ENST00000513801MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-5UTRENST00000409459ENST00000533801MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-intronENST00000352297ENST00000509150MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-intronENST00000393223ENST00000509150MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
5UTR-intronENST00000409459ENST00000509150MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
intron-5UTRENST00000484818ENST00000328560MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
intron-5UTRENST00000484818ENST00000359644MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
intron-5UTRENST00000484818ENST00000393221MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
intron-5UTRENST00000484818ENST00000422190MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
intron-5UTRENST00000484818ENST00000428331MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
intron-5UTRENST00000484818ENST00000504381MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
intron-5UTRENST00000484818ENST00000504948MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
intron-5UTRENST00000484818ENST00000505330MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
intron-5UTRENST00000484818ENST00000507488MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
intron-5UTRENST00000484818ENST00000508532MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
intron-5UTRENST00000484818ENST00000510168MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
intron-5UTRENST00000484818ENST00000513801MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
intron-5UTRENST00000484818ENST00000533801MTMR2chr11

95657037

-ATP2C1chr3

130649258

+
intron-intronENST00000484818ENST00000509150MTMR2chr11

95657037

-ATP2C1chr3

130649258

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for MTMR2-ATP2C1


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.
genomic feature of top 1%

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Fusion Protein Features for MTMR2-ATP2C1


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:95657037/:130649258)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
MTMR2

Q13614

ATP2C1

P98194

FUNCTION: Phosphatase that acts on lipids with a phosphoinositol headgroup. Has phosphatase activity towards phosphatidylinositol 3-phosphate and phosphatidylinositol 3,5-bisphosphate (PubMed:11733541, PubMed:12668758, PubMed:21372139, PubMed:14690594). Binds phosphatidylinositol 4-phosphate, phosphatidylinositol 5-phosphate, phosphatidylinositol 3,5-bisphosphate and phosphatidylinositol 3,4,5-trisphosphate (By similarity). Stabilizes SBF2/MTMR13 at the membranes (By similarity). Specifically in peripheral nerves, stabilizes SBF2/MTMR13 protein (By similarity). {ECO:0000250|UniProtKB:Q9Z2D1, ECO:0000269|PubMed:11733541, ECO:0000269|PubMed:12668758, ECO:0000269|PubMed:14690594, ECO:0000269|PubMed:21372139}.FUNCTION: This magnesium-dependent enzyme catalyzes the hydrolysis of ATP coupled with the transport of the calcium.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page


* Minus value of BPloci means that the break pointn is located before the CDS.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for MTMR2-ATP2C1


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for MTMR2-ATP2C1


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for MTMR2-ATP2C1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for MTMR2-ATP2C1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource